Computational protocol: Genetic analysis of hantaviruses carried by Myodes and Microtus rodents in Buryatia

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Protocol publication

[…] To infer phylogenies, the PHYLIP program package [] was used. Hantavirus sequences used for comparison were recovered from the GenBank. 500 bootstrap replicates generated for complete coding sequences of the S segment, as well as partial sequences of the M segment (Seqboot program) were submitted to the distance matrice algorithm (Dnadist). Distance matrices were analyzed with the Fitch-Margoliash tree-fitting algorithm (Fitch) or with Neighbor-joining algorithm (Neighbor) using the ML model for nucleotide substitutions; the bootstrap support values were calculated with the Consense program. The nucleotide sequence data were also analyzed using the Tree-Puzzle program (maximum likelihood) [] with the HKY model for nucleotide substitutions and 10 000 puzzling steps. […]

Pipeline specifications

Software tools PHYLIP, TREE-PUZZLE
Application Phylogenetics
Organisms Myodes rufocanus, , Myodes regulus